Statistical thermodynamics of biomembranes

Simulation Best Practices for Lipid Membranes [Article v1.0]

We establish a reliable and robust standardization of settings for practical molecular dynamics (MD) simulations of pure and mixed (single- and multi-component) lipid bilayer membranes. In lipid membranes research, particle-based molecular simulations are a powerful tool alongside continuum theory, lipidomics, and model, in vitro, and in vivo experiments. Molecular simulations can provide precise and reproducible spatiotemporal (atomic- and femtosecond-level) information about membrane structure, mechanics, thermodynamics, kinetics, and dynamics. Yet the simulation of lipid membranes can be a daunting task, given the uniqueness of lipid membranes relative to conventional liquid-liquid and solid-liquid interfaces, the immense and complex thermodynamic and statistical mechanical theory, the diversity of multiscale lipid models, limitations of modern computing power, the difficulty and ambiguity of simulation controls, finite size effects, competitive continuum simulation alternatives, and the desired application, including vesicle experiments and biological membranes. These issues can complicate an essential understanding of the field of lipid membranes, and create major bottlenecks to simulation advancement. In this article, we clarify these issues and present a consistent, thorough, and user-friendly framework for the design of state-of-the-art lipid membrane MD simulations. We hope to allow early-career researchers to quickly overcome common obstacles in the field of lipid membranes and reach maximal impact in their simulations.

Foundations of modeling in cryobiology-I: concentration, Gibbs energy, and chemical potential relationships

Mathematical modeling plays an enormously important role in understanding the behavior of cells, tissues, and organs undergoing cryopreservation. Uses of these models range from explanation of phenomena, exploration of potential theories of damage or success, development of equipment, and refinement of optimal cryopreservation/cryoablation strategies. Over the last half century there has been a considerable amount of work in bio-heat and mass-transport, and these models and theories have been readily and repeatedly applied to cryobiology with much success. However, there are significant gaps between experimental and theoretical results that suggest missing links in models. One source for these potential gaps is that cryobiology is at the intersection of several very challenging aspects of transport theory: it couples multi-component, moving boundary, multiphase solutions that interact through a semipermeable elastic membrane with multicomponent solutions in a second time-varying domain, during a two-hundred Kelvin temperature change with multi-molar concentration gradients and multi-atmosphere pressure changes. In order to better identify potential sources of error, and to point to future directions in modeling and experimental research, we present a three part series to build from first principles a theory of coupled heat and mass transport in cryobiological systems accounting for all of these effects. The hope of this series is that by presenting and justifying all steps, conclusions may be made about the importance of key assumptions, perhaps pointing to areas of future research or model development, but importantly, lending weight to standard simplification arguments that are often made in heat and mass transport. In this first part, we review concentration variable relationships, their impact on choices for Gibbs energy models, and their impact on chemical potentials.

Membrane-targeting approaches for enhanced cancer cell destruction with irreversible electroporation

Irreversible electroporation (IRE) is a promising technology to treat local malignant cancer using short, high-voltage electric pulses. Unfortunately, in vivo studies show that IRE suffers from an inability to destroy large volumes of cancer tissue without introduction of cytotoxic agents and/or increasing the applied electrical dose to dangerous levels. This research will address this limitation by leveraging membrane-targeting mechanisms that increase lethal membrane permeabilization. Methods that directly modify membrane properties or change the pulse delivery timing are proposed that do not rely on cytotoxic agents. This work shows that significant enhancement (67-75% more cell destruction in vitro and >100% treatment volume increase in vivo) can be achieved using membrane-targeting approaches for IRE cancer destruction. The methods introduced are surfactants (i.e., DMSO) and pulse timing which are low cost, non-toxic, and easy to be incorporated into existing clinical use. Moreover, when needed, these methods can also be combined with electrochemotherapy to further enhance IRE treatment efficacy.

Introduction to the special issue: Thermodynamic aspects of cryobiology

This brief paper introduces the subject of thermodynamics and the papers of the special issue on thermodynamic aspects of cryobiology. Thermodynamic terminology is defined for the non-specialist.